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PEDIA-Charite / PEDIA-workflow

PEDIA-workflow prioritizes the disease-causing gene by integrating facial analysis and exome sequencing data.
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Implementing Diagnosis Parsing and more QC stats #63

Closed xiamaz closed 6 years ago

xiamaz commented 6 years ago

Differential diagnosis will not count as diagnosis. Thus the three cases with only differential diagnosis will now be excluded by QC. If possible, we should manually correct them. Otherwise QC output is not changed.

To use the new version json_check_failed.log, json_check_failed.log.old, quality_check.log, quality_check.log.old will need to be moved or deleted.

All logs are now of format

{
SECTION: {
    case_id: { info, other data ... }
}
}

This is also used to directly generate a summary of changes between QC runs. This only works using the new format. If old mixed format files are found, it will cause the report generation to crash.

la60312 commented 6 years ago

I have a question about config.yml. I don't know if it relates to this pull request. 118060 is labeled as FAIL due to multi diagnosis. However, it is still in config.yml. Is it because you consider the ID in previous config.yml are all pass? Or should I remove some cache file or remove all the json?

xiamaz commented 6 years ago

config.yml is generated from the folder containing the files since the initial implementation. If cases fail after passing, the vcfs will still be in that folder. So you would have to delete the vcf file.